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  1. Jalview
  2. JAL-2782

potential exception point when viewing structure in Chimera

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Won't Fix
    • Affects Version/s: 2.10.3
    • Fix Version/s: None
    • Component/s: Structures
    • Labels:
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      Description

      During a protracted session of loading large structures and having Chimera time out whilst trying to display or colour them, I noticed NumberFormatException's being raised from the Chimera mapping code. Tracked it down to a routine in jalview.ext.rbvi.strucviz2.ChimeraResidue:

        public void splitInsertionCode(String residue)
        {
          // OK, split the index into number and insertion code
          Pattern p = Pattern.compile("(\\d*)([A-Z]?)");
          Matcher m = p.matcher(residue);
          if (m.matches())
          {
            this.residueNumber = Integer.parseInt(m.group(1));

      Presumably, 'residue' was an empty string, which caused the parseInt to fail.

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Updated:
              Resolved: